AUTHOR=Bruno Alfredo , de Mora Doménica , Rojas-Estevez Paola , Ruiz-Moreno Héctor Alejandro , Guzman-Otazo Jessica , Cáceres Omar , Jiménez Vásquez Victor Alberto , Garcés Jimmy , Olmedo Maritza , Franco-Muñoz Carlos , Medrano Romero Veronica , Fortun Fernandez Evelin Esther , Castro Cusicanqui Maria Renee , Garcia-Bereguiain Miguel Angel ,  “Grupo Andino de Vigilancia Genómica de SARS-CoV-2” , del Carmen Calle Dávila María , Osorio Marisela Mallqui , More Luis Beingolea , Peláez-Carvajal Perú; Dioselina , Vargas Daniel Martínez , Rosales Alicia , De arco-Rodriguez Beatriz Elena , Perez-Lozada Jhindy Tatiana , Chivatá-Ávila Jaime Alexander , Barandica Natalya , Cobos Tatiana , Laiton-Donato Katherine , Álvarez-Díaz Diego A. 

TITLE=Genomic surveillance of SARS-CoV-2 in the Andean Community (2020–2024): integrating regional sequencing efforts from Colombia, Ecuador, Peru, and Bolivia through “ORAS-CONHU” program

JOURNAL=Frontiers in Public Health

VOLUME=Volume 13 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2025.1623413

DOI=10.3389/fpubh.2025.1623413

ISSN=2296-2565

ABSTRACT=IntroductionThe COVID-19 pandemic has deeply affected Latin American countries, with countless COVID-19 cases and deaths. In countries like Peru, Colombia, Ecuador and Bolivia there was a collapse of the public health system, and the lack of testing capacity did not allow to control the spread of SARS-CoV-2 during the first year of the COVID-19 pandemic. After these dramatic beginnings, regional efforts focused on improving testing capacity and massive vaccinations campaigns, but also implementing a sustained SARS-CoV-2 genomic surveillance program to follow up the evolution of the virus.MethodsThis study examines the regional efforts in the Andean Community in terms of SARS-CoV-2 genomic surveillance for Colombia, Ecuador, Peru, and Bolivia in coordination with “Organismo Andino de Salud-Convenio Hipólito Unanue” (ORAS-CONHU). Moreover, SARS-CoV-2 emerging lineages distribution, clade determination and phylogenetic analysis in those countries for the period 2020–2024 was done by retrieving 16,867 sequences from the GISAID database.ResultsFrom the initial lineages 19A and 19B, lineages 20A, 20B, and 20C emerged in 2020, followed by several variants such as 20 J (Gamma), 21A (Delta), 21G (Lambda), and 21H (Mu) emergence along 2021; by the end of 2022, the highly transmissible Omicron variants (21 K, 21 L) emerged and have been evolving into multiple sub variants lineages like 22F, 23A, and 23I (JN.1), the latest dominant along 2024.DiscussionWhile each country exhibits some specific characteristics, the phylogenetic analysis underscored a common pattern in the lineage evolution of SARS-CoV-2 in the Andean Community supporting a rapid transnational transmission of the virus. This study was part of a regional effort to develop an integrative transnational genomic surveillance network for SARS-CoV-2 as a proxy for a more ambitious regional infectious diseases genomic surveillance program.